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ADHOC_TAGSETS_PARAM='a'
ANALYSIS_VIEW="redirect:/myAnalisysList.htm"
AND=4
AND=4
AUTOFLUSH=false
BadFile=3
BadModule=4
BadParameter=2
BadRunnerParams=5
BATCH_SIZE=100000
BATCH_SIZE_PARAM='b'
BENCHMARKING_BATCH_SIZE=20000
BENCHMARKING_BATCH_SIZE=20000
BRACKET_CLOSE=5
BRACKET_CLOSE=5
BRACKET_OPEN=6
BRACKET_OPEN=6
BUFFERSIZE=500*1024
BYTEA=1
BYTEA=1
BYTEA=1
CHECK="check"
CHECK="check"
COMMENT_EOL=7
COMMENT_EOL=7
COMMENT_INLINE=8
COMMENT_INLINE=8
COMPLETED="completed"
COMPRESSED_PARAM='c'
CONSEQUENCE=60
CONST_AT_SIGN="@"
CONTIGPOSITION=50
COVERAGE=40
JAXBElement<AnalysisType>}
AnalysisSet
AnalysisType
AnalysisType.ANALYSISATTRIBUTES
AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
AnalysisType.ANALYSISFILES
AnalysisType.ANALYSISFILES.FILE
AnalysisType.ANALYSISLINKS
AnalysisType.ANALYSISLINKS.ANALYSISLINK
AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
AnalysisType.ANALYSISTYPE
AnalysisType.PARENT
AnalysisType.PARENT.EXPERIMENTREF
AnalysisType.PARENT.RUNREF
AnalysisType.PARENT.SAMPLEPOOLREF
AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
AnalysisType.PARENT.SAMPLEREF
AnalysisType.PARENT.STUDYREF
JAXBElement<ExperimentType>}
ExperimentSet
ExperimentType
ExperimentType.DESIGN
ExperimentType.DESIGN.LIBRARYDESCRIPTOR
ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
ExperimentType.DESIGN.SAMPLEDESCRIPTOR
ExperimentType.DESIGN.SPOTDESCRIPTOR
ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
ExperimentType.EXPERIMENTATTRIBUTES
ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
ExperimentType.EXPERIMENTLINKS
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
ExperimentType.PLATFORM
ExperimentType.PLATFORM.ABISOLID
ExperimentType.PLATFORM.ABISOLID.COLORMATRIX
ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
ExperimentType.PLATFORM.HELICOS
ExperimentType.PLATFORM.ILLUMINA
ExperimentType.PLATFORM.LS454
ExperimentType.PROCESSING
ExperimentType.PROCESSING.BASECALLS
ExperimentType.PROCESSING.QUALITYSCORES
ExperimentType.STUDYREF
JAXBElement<RunType>}
RunSet
RunType
RunType.DATABLOCK
RunType.DATABLOCK.FILES
RunType.DATABLOCK.FILES.FILE
RunType.EXPERIMENTREF
RunType.RUNATTRIBUTES
RunType.RUNATTRIBUTES.RUNATTRIBUTE
RunType.RUNLINKS
RunType.RUNLINKS.RUNLINK
RunType.RUNLINKS.RUNLINK.ENTREZLINK
RunType.RUNLINKS.RUNLINK.URLLINK
JAXBElement<SampleType>}
SampleSet
SampleType
SampleType.MEMBERS
SampleType.MEMBERS.MEMBER
SampleType.SAMPLEATTRIBUTES
SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
SampleType.SAMPLELINKS
SampleType.SAMPLELINKS.SAMPLELINK
SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
SampleType.SAMPLENAME
JAXBElement<StudyType>}
StudySet
StudyType
StudyType.DESCRIPTOR
JAXBElement<String>}
StudyType.DESCRIPTOR.STUDYTYPE
StudyType.STUDYATTRIBUTES
StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
StudyType.STUDYLINKS
StudyType.STUDYLINKS.STUDYLINK
StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
StudyType.STUDYLINKS.STUDYLINK.URLLINK
JAXBElement<SubmissionType>}
SubmissionSet
SubmissionType
SubmissionType.ACTIONS
SubmissionType.ACTIONS.ACTION
SubmissionType.ACTIONS.ACTION.ADD
SubmissionType.ACTIONS.ACTION.HOLD
SubmissionType.ACTIONS.ACTION.MODIFY
SubmissionType.ACTIONS.ACTION.RELEASE
SubmissionType.ACTIONS.ACTION.SUPPRESS
SubmissionType.ACTIONS.ACTION.VALIDATE
SubmissionType.CONTACTS
SubmissionType.CONTACTS.CONTACT
SubmissionType.FILES
SubmissionType.FILES.FILE
CSV_TYPE="csvtype"
CSV_TYPE="csvtype"
DBCOULDNOTDISCONNECT=81
DBCOULDNOTINITIALIZE=80
DEBUG=true
Category.debug(Object).
Category.debug(Object,Throwable).
DELETION=3
DIRECTORYNOTREADABLE=3
DIRECTORYNOTWRITABLE=11
END_ALL_QUERYDATELONG="end-ALL_query-date-long"
END_PMC_QUERYDATELONG="end-PMC_query-date-long"
END_QUAL_QUERYDATELONG="end-QUAL_query-date-long"
ENVVARNOTFOUND=14
EOF=-1
EOF=-1
EQUALS=9
EQUALS=9
Category.error(Object).
Category.error(Object,Throwable).
EXIT_CODE_EXISTING_NAME=5
EXIT_CODE_INVALID_ARGS=1
EXIT_CODE_INVALID_FILE=10
EXPERIMENT_ATTRIBUTES="Header.EXPERIMENT_ATTRIBUTES.getTitle()"
EXPERIMENT_NAME="Header.EXPERIMENT_NAME.getTitle()"
EXPERIMENT_PREFIX="exp_"
EXPERIMENT_SWA="Header.EXPERIMENT_SWA.getTitle()"
EXPERIMENT_TAG_PREFIX="Header.EXPERIMENT_TAG_PREFIX.getTitle()"
EXT_PARAMETERS="ext_parameters"
FAILED="failed"
FAILED="failed"
FAILED="failed"
FAILED="failed"
FAILURE=15
Category.fatal(Object).
Category.fatal(Object,Throwable).
FEATURE=30
FEATURE_SET_ID="FeatureSetID"
FEATURE_SET_PARAM='f'
FEATURE_SET_PARAM='f'
FIELDS=2
FIELDS=2
FIELDS=2
FILE_EXPERIMENT_NAME="f_exp_name"
FILE_EXPERIMENT_NAME="f_exp_name"
FILE_EXPERIMENT_SWID="f_exp_swid"
FILE_EXPERIMENT_SWID="f_exp_swid"
FILE_FILE="f_file"
FILE_FILE="f_file"
FILE_IUS="f_ius"
FILE_IUS="f_ius"
FILE_IUS_NAME="f_ius_name"
FILE_IUS_SWID="f_ius_swid"
FILE_IUS_SWID="f_ius_swid"
FILE_IUS_TAG="f_ius_tag"
FILE_IUS_TAG="f_ius_tag"
FILE_LANE="f_lane"
FILE_LANE="f_lane"
FILE_LANE_NAME="f_lane_name"
FILE_LANE_NAME="f_lane_name"
FILE_LANE_NUMBER="f_lane_num"
FILE_LANE_NUMBER="f_lane_num"
FILE_LANE_SWID="f_lane_swid"
FILE_LANE_SWID="f_lane_swid"
FILE_LIBRARY="f_library"
FILE_LIBRARY="f_library"
FILE_META_TYPE="f_file_meta"
FILE_META_TYPE="f_file_meta"
FILE_PARENT_SAMPLE_NAME="f_sample_name"
FILE_PARENT_SAMPLE_NAME="f_sample_name"
FILE_PARENT_SAMPLE_SWID="f_sample_swid"
FILE_PARENT_SAMPLE_SWID="f_sample_swid"
FILE_PATH="f_file_path"
FILE_PATH="f_file_path"
FILE_PREFIX="fl_"
FILE_PROCESSING_ALG="f_processing_alg"
FILE_PROCESSING_ALG="f_processing_alg"
FILE_PROCESSING_SWID="f_processing_swid"
FILE_PROCESSING_SWID="f_processing_swid"
FILE_RUN_NAME="f_run_name"
FILE_RUN_NAME="f_run_name"
FILE_RUN_SWID="f_run_swid"
FILE_RUN_SWID="f_run_swid"
FILE_SAMPLE="f_sample"
FILE_SAMPLE="f_sample"
FILE_SAMPLE_NAME="f_child_sample_name"
FILE_SAMPLE_NAME="f_child_sample_name"
FILE_SAMPLE_SWID="f_child_sample_swid"
FILE_SAMPLE_SWID="f_child_sample_swid"
FILE_SEQUENCER_NAME="f_seqrun_name"
FILE_SEQUENCER_NAME="f_seqrun_name"
FILE_SEQUENCER_SWID="f_seqrun_swid"
FILE_SEQUENCER_SWID="f_seqrun_swid"
FILE_STUDY_SWID="f_study_swid"
FILE_STUDY_SWID="f_study_swid"
FILE_STUDY_TITLE="f_study_title"
FILE_STUDY_TITLE="f_study_title"
FILE_SWA="Header.FILE_SWA.getTitle()"
FILE_SWID="f_file_swid"
FILE_SWID="f_file_swid"
FILE_TEMPLATE="f_template"
FILE_TEMPLATE="f_template"
FILE_TISSUE="f_tissue"
FILE_TISSUE="f_tissue"
FILE_WF_NAME="f_wf_name"
FILE_WF_NAME="f_wf_name"
FILE_WF_SWID="f_wf_swid"
FILE_WF_SWID="f_wf_swid"
FILE_WF_VERSION="f_wf_version"
FILE_WF_VERSION="f_wf_version"
FILEEMPTY=12
ValidationReportService.fileLinkReport(List) including all files in the SeqWare
meta db.
ValidationReportService.fileLinkReport(List) including all files in the SeqWare
meta db.
FILENOTEXECUTABLE=10
FILENOTREADABLE=4
FILENOTWRITABLE=5
FILETYPE_ALL="all"
FINISHED="completed"
FLOAT=10
FLOAT=10
FOLLOW_26_in_key_value_function293
FOLLOW_26_in_three_param_predicate342
FOLLOW_26_in_three_param_predicate346
FOLLOW_26_in_two_param_predicate317
FOLLOW_AND_in_high_precedence_constraint117
FOLLOW_BRACKET_CLOSE_in_key_value_function297
FOLLOW_BRACKET_CLOSE_in_nested_constraint145
FOLLOW_BRACKET_CLOSE_in_three_param_predicate350
FOLLOW_BRACKET_CLOSE_in_two_param_predicate321
FOLLOW_BRACKET_OPEN_in_key_value_function288
FOLLOW_BRACKET_OPEN_in_nested_constraint140
FOLLOW_BRACKET_OPEN_in_three_param_predicate337
FOLLOW_BRACKET_OPEN_in_two_param_predicate312
FOLLOW_comparison_in_constraint165
FOLLOW_comparison_in_constraint175
FOLLOW_constant_in_constraint168
FOLLOW_constant_in_constraint173
FOLLOW_constraint_in_nested_constraint151
FOLLOW_EOF_in_query78
FOLLOW_high_precedence_constraint_in_low_precedence_constraint91
FOLLOW_high_precedence_constraint_in_low_precedence_constraint98
FOLLOW_ID_in_identifier200
FOLLOW_identifier_in_constraint163
FOLLOW_identifier_in_constraint178
FOLLOW_key_value_function_in_identifier206
FOLLOW_literal_in_constant249
FOLLOW_literal_in_key_value_function291
FOLLOW_literal_in_key_value_function295
FOLLOW_literal_in_three_param_predicate340
FOLLOW_literal_in_three_param_predicate344
FOLLOW_literal_in_three_param_predicate348
FOLLOW_literal_in_two_param_predicate315
FOLLOW_literal_in_two_param_predicate319
FOLLOW_low_precedence_constraint_in_nested_constraint143
FOLLOW_low_precedence_constraint_in_query75
FOLLOW_NAMED_CONSTANT_in_constant254
FOLLOW_NAMED_FUNCTION_in_key_value_function285
FOLLOW_NAMED_THREE_PARAM_PREDICATE_in_three_param_predicate334
FOLLOW_NAMED_TWO_PARAM_PREDICATE_in_two_param_predicate309
FOLLOW_nested_constraint_in_high_precedence_constraint113
FOLLOW_nested_constraint_in_high_precedence_constraint120
FOLLOW_NOT_in_nested_constraint135
FOLLOW_OR_in_low_precedence_constraint95
FOLLOW_three_param_predicate_in_constraint189
FOLLOW_two_param_predicate_in_constraint183
FREEMARKEREXCEPTION=70
abstractStr.
accession.
accession.
accession.
active.
active.
active.
active.
active.
active.
active.
adapters.
adapterSpec.
addedSurcharge.
adhoctagset.
agent.
algorithm.
algorithm.
algorithm.
algorithm.
alias.
alias.
alias.
alias.
allInputFiles.
allItems.
anonymizedName.
arguments.
attribute.
attributes.
attributes.
attributes.
backendTimestamp.
barcode.
baseCaller.
baseCoord.
baseDir.
baseIniFile.
baseQualities.
batch_size.
binSize.
binSize.
blockCount.
blockSizes.
blockStarts.
cacheSize.
calledBase.
calledBaseCount.
calledBaseCountForward.
calledBaseCountReverse.
callOne.
callTwo.
centerName.
centerName.
centerProjectName.
children.
children.
childrenUrls.
childSample.
childSample.
childSample.
childSample.
childSample.
classesDir.
clientNotes.
code.
code.
codingStart.
codingStop.
colorMatrix.
colorMatrix.
colorMatrixCode.
colorMatrixCode.
command.
command.
command.
completed.
computeReq.
configPath.
configuration.
configuration.
confirmEmailAddress.
confirmPassword.
connectionString.
consensusAveSeqQuality.
consensusBase.
consensusCallQuality.
consensusMaxSeqQuality.
constructionProtocol.
contig.
contig.
contig.
contig.
count.
countFile.
coverage.
coverage.
created.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimeStamp.
createTimeStamp.
createTstmp.
createTstmp.
createTstmp.
createTstmp.
createTstmp.
criteria.
currentWorkingDir.
cursor.
cursor.
cwd.
cycleCoord.
cycleCount.
cycleCount.
cycleDescriptor.
cycleDescriptor.
cycleDescriptor.
cycles.
cycles.
cycleSequence.
cycleSequence.
data.
database.
dax.
daysUntilDue.
db.
db.
db.
db.
db.
db.
dbmd.
decodeMethod.
defaultValue.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
directoriesNumber.
display.
displayName.
displayName.
displayName.
displayName.
displayValue.
domainObject.
domainObject.
email.
emailAddress.
end.
endDate.
endPage.
entityUrl.
error.
errorCount.
existingType.
existingTypeInt.
exitStatus.
exitStatus.
expectedBaseCall.
expectedNumberReads.
expectedNumberRuns.
expectedNumberSpots.
expectedNumReads.
expectedNumRuns.
expectedNumSpots.
expenseId.
expenses.
expenseType.
experiment.
experiment.
experiment.
experiment.
experiment.
experiment.
experimentAttributeId.
experimentAttributes.
experimentId.
experimentLibraryDesign.
experimentLibraryDesignId.
experimentLibraryDesignService.
experimentLinkId.
experimentLinks.
experiments.
experiments.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentSpotDesign.
experimentSpotDesign.
experimentSpotDesignId.
experimentSpotDesignReadSpecId.
experimentSpotDesignReadSpecService.
experimentSpotDesignService.
expLibDesignDesc.
expLibDesignName.
expLibDesignProtocol.
expLibDesignSelection.
expLibDesignSource.
expLibDesignStrategy.
expSpotDesignAdapterSpec.
expSpotDesignReadsPerSpot.
expSpotDesignTagSpec.
extension.
externalId.
failed.
fastqConvNum.
fastqConvNum.
feature.
featureSetID.
file.
file.
file.
file.
file.
fileAttributeId.
fileAttributes.
fileAttributeService.
fileId.
fileMetaType.
fileMetaType.
fileOne.
filePath.
filePath.
filePath.
filePath.
filePath.
filePath.
files.
files.
files.
files.
files_url.
filesArray.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
filesNumber.
fileTwo.
fileTwoURL.
fileType.
fileType.
fileType.
fileTypeId.
fileTypeId.
fileTypeId.
fileTypeService.
fileTypeService.
fileTypeService.
fileTypeService.
fileTypeService.
fileTypeService.
fileUploadService.
fileURL.
fileURL.
finishedTimestamp.
firstName.
firstName.
flowCount.
flowCount.
flowSequence.
flowSequence.
folderStore.
folderStore.
frame.
friendlyRowKey.
fuzzyStartPositionMax.
fuzzyStopPositionMin.
geneChr.
geneId.
geneId.
genomeId.
genomicSequence.
group.
host.
host.
html.
html.
html.
id.
id.
id.
id.
id.
id.
id.
id.
id.
id.
identitySamples.
immediateInputFiles.
individualName.
info.
iniFile.
input.
input.
inputAlgorithm.
institution.
institution.
instrumentModel.
instrumentName.
instrumentName.
invitationCode.
invoice.
invoiceId.
invoiceService.
invoiceService.
isEnd.
isHasFile.
isHasFile.
isHasFile.
isHasFile.
isHasFile.
isHasFile.
isHasFile.
isInvitationCode.
isSelected.
isSelected.
isSelected.
isSelected.
isSelected.
isSelected.
isSelected.
isSelected.
isStart.
itemRgb.
ius.
ius.
ius.
ius.
ius.
ius.
ius.
ius.
ius.
ius.
iusAttributeId.
iusAttributes.
iusId.
iusLinkId.
iusLinks.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
joinDevelopersMailingList.
joinUsersMailingList.
key.
key.
key.
key.
keyIndex.
keyvalues.
label.
label.
label.
label.
label.
label.
label.
label.
label.
label.
label.
lane.
lane.
lane.
lane.
lane.
lane.
lane.
lane.
lane.
lane1.
lane2.
lane3.
lane4.
lane5.
lane6.
lane7.
lane8.
lane_url.
laneAttributeId.
laneAttributes.
laneCount.
laneId.
laneIndex.
laneLinkId.
laneLinks.
lanes.
lanes.
lanes.
lanes.
lanes.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
lastName.
lastName.
layout.
length.
libraryId.
librarySamples.
librarySelectionId.
librarySelectionService.
librarySelectionService.
libraryService.
librarySourceId.
librarySourceService.
librarySourceService.
libraryStrategyId.
libraryStrategyService.
libraryStrategyService.
libraryType.
map.
maxCoverage.
maxCoverage.
maxCoverage.
maximumMappingQuality.
maxLockers.
maxLockObjects.
maxLocks.
md5sum.
md5sum.
memReq.
metadata.
metadata.
metaType.
metaType.
metaType.
minCoverage.
minCoverage.
minCoverage.
minObservations.
minObservationsPerStrand.
minPercent.
minSnpQuality.
minSnpQuality.
minSNVPhred.
mismatchAAChangeBlosumScore.
mismatchAminoAcidChange.
mismatchChr.
mismatchCodonChange.
mismatchCodonPosition.
mismatches.
mismatches.
mismatchId.
mismatchStart.
mismatchStop.
mismatchType.
moduleType.
mutatedGenomicSequence.
mutatedTranslatedSequence.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
nameNode.
ncbiTaxId.
ncbiTaxonomyId.
networkReq.
newType.
nominalLength.
nominalSdev.
notes.
notRunned.
offspringProcessings.
organism.
organism.
organism.
organismId.
organismId.
organismService.
organismService.
originalFileName.
output.
outputDir.
outputFilename.
outputFilename.
outputFiles.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
ownerId.
page.
paidAmount.
pairedEnd.
pairedEnd.
pairedFilePath.
pairedFilePath.
pairedOrientation.
parameters.
parameters.
parameters.
params.
parentProcessingAccession.
parentProcessings.
parents.
parents.
parentUrls.
password.
password.
passwordHint.
pathToFirstFile.
pathToSecondFile.
pending.
permanentBundleLocation.
permBundleLocation.
platform.
platform.
platform.
platformId.
platformInt.
platformInt.
platformService.
platformService.
platformService.
platformService.
platformService.
pmi.
pmi.
postgresqlPersistenceStrategy.
pricePerUnit.
pricePerUnit.
process.
processedCount.
processExitStatus.
processExitStatus.
processing.
processing.
processing.
processing.
processing.
processing.
processing.
processing.
processing.
processingAccession.
processingAttributeId.
processingAttributes.
processingByChildId.
processingByParentId.
processingCount.
processingExperimentsId.
processingExperimentsService.
processingId.
processingIusId.
processingIusService.
processingLaneService.
processingLanesId.
processingRelationshipId.
processingRelationshipService.
processings.
processings.
processings.
processings.
processings.
processings.
processings.
processings.
processings.
processingSamplesId.
processingSamplesService.
processingSequencerRunService.
processingSequencerRunsId.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingStudiesId.
processingStudiesService.
projectId.
projectId.
qualityMultiplier.
qualityNumberOfLevels.
qualityScorer.
qualityType.
readBases.
readClass.
readCount.
reader.
readIndex.
readLabel.
readSpec.
readSpecs.
readsPerSpot.
readsSupportingCallOne.
readsSupportingCallThree.
readsSupportingCallTwo.
readType.
readyToProcess.
referenceAveSeqQuality.
referenceBase.
referenceCallQuality.
referenceId.
referenceMaxSeqQuality.
referenceName.
refLane.
refLane.
regions.
regions.
registration.
registration.
registration.
registration.
registration.
registration.
registration.
registrationId.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
relationship.
relativeLocation.
returnValue.
returnValue.
returnValues.
rootSample.
rowId.
rowId.
rows.
runCenter.
runCenter.
runStartTimestamp.
runStartTstmp.
runStopTimestamp.
runStopTstmp.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample_url.
sampleAttributeId.
sampleAttributes.
sampleCode.
sampleId.
sampleId.
sampleId.
sampleLinkId.
sampleLinks.
sampleReportService.
samples.
samples.
samples.
samples.
sampleSearch.
sampleSearchAttributeId.
sampleSearchAttributes.
sampleSearchId.
sampleSearchService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleType.
sampleUrl.
score.
selection.
sender.
sequencer_run_url.
sequencerRun.
sequencerRun.
sequencerRun.
sequencerRun.
sequencerRun.
sequencerRunAttributeId.
sequencerRunAttributes.
sequencerRunId.
sequencerRunId.
sequencerRuns.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunValidator.
sequencerRunWizardValidator.
sequenceSpace.
seqwareRevision.
seqwareVersion.
serialVersionUID.
serialVersionUID.
serialVersionUID.
serialVersionUID.
serialVersionUID.
serialVersionUID.
serialVersionUID.
serialVersionUID.
serialVersionUID.
serialVersionUID.
serialVersionUID.
serialVersionUID.
server.
sessionFactory.
settings.
settings.
settings.
sharedStudies.
sharedWorkflowRuns.
shareExperimentId.
shareFileId.
shareLaneId.
shareProcessingId.
shareSampleId.
shareStudyId.
shareStudyService.
shareStudyService.
shareWorkflowRunId.
shareWorkflowRunService.
shareWorkflowRunService.
site.
size.
size.
skip.
skip.
skip.
skip.
skip.
skipTxt.
slideOneFilePath.
slideOneFilePath.
slideOneLaneCount.
slideOneLaneCount.
slideTwoFilePath.
slideTwoFilePath.
slideTwoLaneCount.
slideTwoLaneCount.
sortKeySample.
source.
source.
spotDesignReadSpec.
sql.
start.
startDate.
startPage.
startPosition.
startPosition.
startPosition.
state.
stats.
status.
status.
status.
status.
status.
status.
status.
status.
statusCmd.
statusCounts.
statuses.
stderr.
stdErr.
stderr.
stdout.
stdOut.
stdout.
stop.
stopPosition.
stopPosition.
stopPosition.
store.
store.
store.
storeType.
strand.
strand.
strategy.
strExpectedNumberReads.
strExpectedNumberRuns.
strExpectedNumReads.
strExpectedNumRuns.
strLaneCount.
strRefLane.
strStartURL.
strStartURL.
studies.
study.
study.
study.
study.
study.
study.
study.
studyAttributeId.
studyAttributes.
studyDAO.
studyId.
studyId.
studyLinkId.
studyLinks.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyTypeDAO.
studyTypeId.
studyTypeService.
studyTypeService.
subjectEmail.
sum.
summaryLines.
svType.
swa.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
tag.
tag.
tag.
tag.
tag.
tags.
tags.
tags.
tags.
tagSetIDs.
tagSpec.
template.
template.
templateEmail.
templateFile.
templatePath.
templateType.
testCmd.
thickEnd.
thickStart.
timeTaken.
tissSource.
title.
title.
title.
tokenNames.
total.
totalPrice.
totalPrice.
totalUnits.
transcriptId.
translatedSequence.
translocationDestinationContig.
translocationDestinationStartPosition.
translocationDestinationStopPosition.
translocationType.
type.
type.
type.
type.
type.
type.
type.
type.
typeNode.
unit.
units.
units.
units.
units.
units.
units.
units.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimeStamp.
updateTimeStamp.
updateTstmp.
updateTstmp.
updateTstmp.
updateTstmp.
updateTstmp.
updateValidator.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
urlLabel.
urlLabel.
urlLabel.
urlString.
useIparIntensities.
useIparIntensities.
useOneURL.
username.
userName.
username.
useTwoURL.
useURL.
validationReportService.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
value.
value.
value.
value.
value.
value.
value.
value.
value.
value.
values.
version.
version.
version.
version.
visibleParams.
wfRuns.
workerName.
workerName.
workflow.
workflow.
workflow.
workflow.
workflowAccession.
workflowAttributeId.
workflowAttributes.
workflowDir.
workflowId.
workflowParam.
workflowParamId.
workflowParamId.
workflowParams.
workflowParamService.
workflowParamService.
workflowParamService.
workflowParamService.
workflowParamValueId.
workflowParamValueService.
workflowParamValueService.
workflowParamValueService.
workflowRun.
workflowRun.
workflowRun.
workflowRun.
workflowRun.
workflowRunAttributeId.
workflowRunAttributes.
workflowRunByAncestorWorkflowRunId.
workflowRunId.
workflowRunId.
workflowRunId.
workflowRunParams.
workflowRunProcessings.
workflowRuns.
workflowRuns.
workflowRuns.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
zygosity.
GFF3_DELETION="deletion"
GFF3_INSERTION="insertion"
GFF3_SNV="VCF_SNV"
GFF3_UNKNOWN_TYPE="unknown_type"
GT=11
GT=11
GTEQ=12
GTEQ=12
GVF_ALIAS="Alias"
GVF_BREAKPOINT_DETAIL="Breakpoint_detail"
GVF_DBXREF="Dbxref"
GVF_END_RANGE="End_range"
GVF_GENOTYPE="Genotype"
GVF_HEMIZYGOUS="hemizygous"
GVF_HETEROZYGOUS="heterozygous"
GVF_HOMOZYGOUS="homozygous"
GVF_INDIVIDUAL="Individual"
GVF_PHASED="Phased"
GVF_REFERENCE_AA="Reference_aa"
GVF_REFERENCE_CODON="Reference_codon"
GVF_REFERENCE_SEQ="Reference_seq"
GVF_SEQUENCE_CONTEXT="Sequence_context"
GVF_START_RANGE="Start_range"
GVF_TOTAL_READS="Total_reads"
GVF_VARIANT_AA="Variant_aa"
GVF_VARIANT_CODON="Variant_codon"
GVF_VARIANT_EFFECT="Variant_effect"
GVF_VARIANT_FREQ="Variant_freq"
GVF_VARIANT_READS="Variant_reads"
GVF_VARIANT_SEQ="Variant_seq"
GVF_ZYGOSITY="Zygosity"
HEMIZYGOUS=3
HETEROZYGOUS=2
HG_19="hg_19"
HG_19="hg_19"
HOMOZYGOUS=1
ID=13
ID=13
Category.info(Object).
Category.info(Object,Throwable).
INPUT_FILES_PARAM='i'
INSERTION=2
INT=14
INT=14
INT_PARAMETERS="int_parameters"
INVALIDARGUMENT=9
INVALIDFILE=7
INVALIDPARAMETERS=2
INVALIDPLUGIN=120
IUS_ATTRIBUTES="Header.IUS_ATTRIBUTES.getTitle()"
IUS_PREFIX="ius_"
IUS_SWA="Header.IUS_SWA.getTitle()"
IUS_TAG="Header.IUS_TAG.getTitle()"
IUS_TAG_PREFIX="Header.IUS_TAG_PREFIX.getTitle()"
JSON="json"
JSON="json"
KEYVALUE_OUT_PARAM='k'
LANE_ATTRIBUTES="Header.LANE_ATTRIBUTES.getTitle()"
LANE_NAME="Header.LANE_NAME.getTitle()"
LANE_NUM="Header.LANE_NUM.getTitle()"
LANE_PREFIX="seq_"
LANE_SWA="Header.LANE_SWA.getTitle()"
LANE_TAG_PREFIX="Header.LANE_TAG_PREFIX.getTitle()"
LT=15
LT=15
LTEQ=16
LTEQ=16
MAX_BASE=94
maxThreads=Integer.parseInt(EnvUtil.getProperty("maxconnections"))
MAXVERSIONS=1000
METADATAINVALIDIDCHAIN=8
MINUS_STRAND=2
AtomImpl)NAME="ExperimentLibraryDesignService"
NAME="ExperimentService"
NAME="ExperimentSpotDesignReadSpecService"
NAME="ExperimentSpotDesignService"
NAME="fileService"
NAME="FileTypeService"
NAME="FileUploadService"
NAME="invoiceService"
NAME="IUSService"
NAME="laneService"
NAME="LibrarySelectionService"
NAME="LibrarySourceService"
NAME="LibraryStrategyService"
NAME="OrganismService"
NAME="PlatformService"
NAME="processingService"
NAME="projectService"
NAME="registrationService"
NAME="sampleService"
NAME="SequencerRunService"
NAME="shareStudyService"
NAME="shareWorkflowRunService"
NAME="StudyService"
NAME="StudyTypeService"
NAME="workflowParamService"
NAME="WorkflowParamValueService"
NAME="WorkflowRunParamService"
NAME="WorkflowRunService"
NAME="WorkflowService"
NAMED_CONSTANT=17
NAMED_CONSTANT=17
NAMED_FUNCTION=18
NAMED_FUNCTION=18
NAMED_THREE_PARAM_PREDICATE=19
NAMED_THREE_PARAM_PREDICATE=19
NAMED_TWO_PARAM_PREDICATE=20
NAMED_TWO_PARAM_PREDICATE=20
NO_STRAND=0
NOT=21
NOT=21
NOTEQUALS=22
NOTEQUALS=22
NOTIMPLEMENTED=-1
NULL=-99
NULLIZYGOUS=4
NUMBER_THREADS_PARAM='t'
OID=0
OID=0
OID=0
OR=23
OR=23
OUTPUT_FILE_PARAM='o'
OUTPUTFILE_PARAM='o'
PAD=15
PAD=15
PAGE_NUM="page"
PAGE_NUM="page"
PARENT_SAMPLE_ATTRIBUTES="Header.PARENT_SAMPLE_ATTRIBUTES.getTitl"{trunked}
PARENT_SAMPLE_NAME="Header.PARENT_SAMPLE_NAME.getTitle()"
PARENT_SAMPLE_SWA="Header.PARENT_SAMPLE_SWA.getTitle()"
PARENT_SAMPLE_TAG_PREFIX="Header.PARENT_SAMPLE_TAG_PREFIX.getTitl"{trunked}
PENDING="pending"
PENDING="pending"
PENDING="pending"
PERSIST_VERSION_CHAINS=false
PLUS_STRAND=1
PositionSeparator=":"
Poster class.prefix="FeatureSet"
prefix="Group"
prefix="Feature"
prefix="Plugin"
prefix="PluginRun"
prefix="Reference"
prefix="ReferenceSet"
prefix="Tag"
prefix="TagSet"
prefix="User"
PROCESSING=100
PROCESSING_ALGO="Header.PROCESSING_ALGO.getTitle()"
PROCESSING_ATTRIBUTES="Header.PROCESSING_ATTRIBUTES.getTitle()"
PROCESSING_DATE="Header.PROCESSING_DATE.getTitle()"
PROCESSING_PREFIX="ae_"
PROCESSING_SWID="Header.PROCESSING_SWID.getTitle()"
PROCESSING_TAG_PREFIX="Header.PROCESSING_TAG_PREFIX.getTitle()"
PROGRAMFAILED=1
QUERY_PARAM_FILE='p'
QUERY_PARAM_STRING='s'
QUEUED=101
REFERENCE_ID_PARAM='r'
RESUBMITTED="resubmitted"
RETURNEDHELPMSG=110
ROWS_PER_PAGE="rp"
ROWS_PER_PAGE="rp"
RUNNERERR=91
RUNNING="running"
RUNNING="running"
RUNNING="running"
RUNNING="running"
RUNTIMEEXCEPTION=6
SAMPLE_ATTRIBUTES="Header.SAMPLE_ATTRIBUTES.getTitle()"
SAMPLE_CHILD="s_child"
SAMPLE_NAME="Header.SAMPLE_NAME.getTitle()"
SAMPLE_PREFIX="sam_"
SAMPLE_SAMPLE="s_sample"
SAMPLE_SWA="Header.SAMPLE_SWA.getTitle()"
SAMPLE_SWID="sw"
SAMPLE_TAG_PREFIX="Header.SAMPLE_TAG_PREFIX.getTitle()"
SEARCH_CASE_SENSITIVE="search.checked"
SECONDARY_INDEX="sIndex.out"
SECONDARY_INDEX_HACK=false
SECONDARY_INDEX_PARAM='x'
SELECTED_FILES="selectedLaunchFiles"
SELECTED_NODES="launchSelectedNodes"
SELECTED_VALUES="selectedWorkflowParamValueId"
SEPARATOR="."
SEPARATOR="::"
SEPARATOR="java.io.File.separator"
SEPARATOR="java.io.File.separator"
SEQ_RUN_ID="seq_run_id"
SEQUENCER_RUN_ATTRIBUTES="Header.SEQUENCER_RUN_ATTRIBUTES.getTitl"{trunked}
SEQUENCER_RUN_NAME="Header.SEQUENCER_RUN_NAME.getTitle()"
SEQUENCER_RUN_SWA="Header.SEQUENCER_RUN_SWA.getTitle()"
SEQUENCER_RUN_TAG_PREFIX="Header.SEQUENCER_RUN_TAG_PREFIX.getTitl"{trunked}
SEQUENCER_VIEW="redirect:/sequencerRunList.htm"
SEQWARE_SETTINGS_PROPERTY="SEQWARE_SETTINGS"
abstractStr.
accession.
accession.
accession.
active.
active.
active.
active.
active.
active.
active.
adapters.
adapterSpec.
addedSurcharge.
adhoctagset.
agent.
algorithm.
algorithm.
algorithm.
alias.
alias.
alias.
alias.
allInputFiles.
allItems.
anonymizedName.
attributes.
attributes.
attributes.
backendTimestamp.
barcode.
baseCaller.
baseCoord.
baseDir.
baseIniFile.
baseQualities.
batch_size.
binSize.
binSize.
blockCount.
blockSizes.
blockStarts.
cacheSize.
calledBase.
calledBaseCount.
calledBaseCountForward.
calledBaseCountReverse.
callOne.
callTwo.
centerName.
centerName.
centerProjectName.
children.
children.
childrenUrls.
childSample.
childSample.
childSample.
childSample.
childSample.
classesDir.
clientNotes.
code.
code.
codingStart.
codingStop.
colorMatrix.
colorMatrix.
colorMatrixCode.
colorMatrixCode.
command.
command.
command.
completed.
compressed.
compressed.
computeReq.
configPath.
confirmEmailAddress.
confirmPassword.
connectionString.
consensusAveSeqQuality.
consensusBase.
consensusCallQuality.
consensusMaxSeqQuality.
constructionProtocol.
contig.
contig.
contig.
contig.
count.
countFile.
coverage.
createConsequenceAnnotationDB.
createCoverageDB.
created.
createDbSNPAnnotationDB.
createMismatchDB.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimestamp.
createTimeStamp.
createTimeStamp.
createTstmp.
createTstmp.
createTstmp.
createTstmp.
createTstmp.
criteria.
currentWorkingDir.
cwd.
cycleCoord.
cycleCount.
cycleCount.
cycleDescriptor.
cycleDescriptor.
cycleDescriptor.
cycles.
cycles.
cycleSequence.
cycleSequence.
data.
database.
dax.
daysUntilDue.
db.
db.
db.
db.
db.
db.
dbmd.
debug.
decodeMethod.
defaultValue.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
description.
display.
displayName.
displayName.
displayName.
displayName.
displayValue.
domainObject.
domainObject.
email.
emailAddress.
end.
endDate.
endPage.
entityUrl.
errorCount.
existingType.
existingTypeInt.
exitCode.
exitStatus.
exitStatus.
expectedBaseCall.
expectedNumberReads.
expectedNumberRuns.
expectedNumberSpots.
expectedNumReads.
expectedNumRuns.
expectedNumSpots.
expenseId.
expenses.
expenseType.
experiment.
experiment.
experiment.
experiment.
experiment.
experiment.
experimentAttributeId.
experimentAttributes.
experimentDAO.
experimentId.
experimentLibraryDesign.
experimentLibraryDesignId.
experimentLibraryDesignService.
experimentLinkId.
experimentLinks.
experiments.
experiments.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentService.
experimentSpotDesign.
experimentSpotDesign.
experimentSpotDesignId.
experimentSpotDesignReadSpecId.
experimentSpotDesignReadSpecService.
experimentSpotDesignService.
expLibDesignDesc.
expLibDesignName.
expLibDesignProtocol.
expLibDesignSelection.
expLibDesignSource.
expLibDesignStrategy.
expSpotDesignAdapterSpec.
expSpotDesignReadsPerSpot.
expSpotDesignTagSpec.
extension.
externalId.
externalSerializationVersion.
failed.
fastqConvNum.
fastqConvNum.
feature.
featureSetID.
file.
file.
file.
file.
file.
fileAttributeId.
fileAttributes.
fileDAO.
fileId.
fileMetaType.
fileMetaType.
fileOne.
filePath.
filePath.
filePath.
filePath.
filePath.
filePath.
fileReportDAO.
fileReportService.
fileReportService.
fileReportService.
files.
files.
files.
files.
files_url.
filesArray.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileService.
fileTwo.
fileTwoURL.
fileType.
fileType.
fileType.
fileTypeDAO.
fileTypeId.
fileTypeId.
fileTypeId.
fileTypeService.
fileTypeService.
fileTypeService.
fileTypeService.
fileTypeService.
fileTypeService.
fileUploadService.
fileURL.
fileURL.
finalized.
finishedTimestamp.
firstName.
firstName.
flowCount.
flowCount.
flowSequence.
flowSequence.
folderStore.
folderStore.
frame.
friendlyRowKey.
friendlyRowKey.
fullyPaid.
fuzzyStartPositionMax.
fuzzyStopPositionMin.
geneChr.
geneId.
geneId.
genomeId.
genomicSequence.
group.
host.
host.
html.
html.
html.
id.
id.
id.
id.
id.
id.
id.
identitySamples.
immediateInputFiles.
includeCoverage.
includeCoverage.
includeIndels.
includeIndels.
includeIndels.
includeSNV.
includeSNV.
includeSNVs.
individualName.
info.
iniFile.
input.
input.
inputAlgorithm.
institution.
institution.
instrumentModel.
instrumentName.
instrumentName.
invitationCode.
invoice.
invoiceId.
invoiceService.
invoiceService.
isEnd.
isHasFile.
isHasFile.
isHasFile.
isHasFile.
isHasFile.
isHasFile.
isHasFile.
isSelected.
isSelected.
isSelected.
isSelected.
isSelected.
isSelected.
isSelected.
isSelected.
isStart.
itemRgb.
ius.
ius.
ius.
ius.
ius.
ius.
ius.
ius.
iusAttributeId.
iusAttributes.
iusId.
iusLinkId.
iusLinks.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
iusService.
jdbcTemplate.
joinDevelopersMailingList.
joinUsersMailingList.
key.
key.
key.
key.
keyIndex.
keyvalues.
label.
label.
label.
label.
label.
label.
label.
label.
label.
label.
label.
lane.
lane.
lane.
lane.
lane.
lane.
lane.
lane.
lane1.
lane2.
lane3.
lane4.
lane5.
lane6.
lane7.
lane8.
lane_url.
laneAttributeId.
laneAttributes.
laneCount.
laneDAO.
laneId.
laneIndex.
laneLinkId.
laneLinks.
lanes.
lanes.
lanes.
lanes.
lanes.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
laneService.
lastName.
lastName.
layout.
length.
libraryId.
librarySamples.
librarySelectionId.
librarySelectionService.
librarySelectionService.
libraryService.
librarySourceId.
librarySourceService.
librarySourceService.
libraryStrategyId.
libraryStrategyService.
libraryStrategyService.
libraryType.
maxCoverage.
maxCoverage.
maxCoverage.
maximumMappingQuality.
maximumMappingQuality.
maxLockers.
maxLockObjects.
maxLocks.
md5sum.
md5sum.
memReq.
metadata.
metadata.
metaType.
metaType.
metaType.
minCoverage.
minCoverage.
minCoverage.
minObservations.
minObservationsPerStrand.
minPercent.
minSnpQuality.
minSnpQuality.
minSNVPhred.
mismatchAAChangeBlosumScore.
mismatchAminoAcidChange.
mismatchChr.
mismatchCodonChange.
mismatchCodonPosition.
mismatchId.
mismatchStart.
mismatchStop.
mismatchType.
moduleParameter.
mutatedGenomicSequence.
mutatedTranslatedSequence.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
name.
nameNode.
ncbiTaxId.
ncbiTaxonomyId.
networkReq.
newType.
nominalLength.
nominalSdev.
notes.
notRunned.
offspringProcessings.
organism.
organism.
organism.
organismId.
organismId.
organismService.
organismService.
originalFileName.
outputDir.
outputFilename.
outputFilename.
outputFiles.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
owner.
ownerId.
page.
paidAmount.
pairedEnd.
pairedEnd.
pairedFilePath.
pairedFilePath.
pairedOrientation.
parameters.
parameters.
params.
parentProcessingAccession.
parentProcessings.
parents.
parents.
parentUrls.
password.
password.
passwordHint.
pathToFirstFile.
pathToSecondFile.
payee.
pending.
permanentBundleLocation.
permBundleLocation.
platform.
platform.
platform.
platformId.
platformInt.
platformInt.
platformService.
platformService.
platformService.
platformService.
platformService.
pmi.
pmi.
postgresqlPersistenceStrategy.
pricePerUnit.
process.
processedCount.
processExitStatus.
processExitStatus.
processing.
processing.
processing.
processing.
processing.
processing.
processing.
processing.
processing.
processingAccession.
processingAttributeId.
processingAttributes.
processingByChildId.
processingByParentId.
processingCount.
processingDAO.
processingDAO.
processingExperimentsId.
processingExperimentsService.
processingId.
processingIusId.
processingIusService.
processingLaneService.
processingLanesId.
processingRelationshipId.
processingRelationshipService.
processings.
processings.
processings.
processings.
processings.
processings.
processings.
processings.
processings.
processingSamplesId.
processingSamplesService.
processingSequencerRunService.
processingSequencerRunsId.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingService.
processingStudiesId.
processingStudiesService.
projectId.
projectId.
qualityMultiplier.
qualityNumberOfLevels.
qualityScorer.
qualityType.
readBases.
readClass.
readCount.
reader.
readIndex.
readLabel.
readOnly.
readSpec.
readSpecs.
readsPerSpot.
readsSupportingCallOne.
readsSupportingCallThree.
readsSupportingCallTwo.
readType.
readyToProcess.
referenceAveSeqQuality.
referenceBase.
referenceCallQuality.
referenceId.
referenceMaxSeqQuality.
refLane.
refLane.
regions.
regions.
registration.
registration.
registration.
registration.
registration.
registration.
registration.
registrationId.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
registrationService.
relationship.
relativeLocation.
requireFiles.
returnIds.
returnValue.
returnValue.
rootSample.
rowId.
rowId.
rows.
runCenter.
runCenter.
runStartTimestamp.
runStartTstmp.
runStopTimestamp.
runStopTstmp.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample.
sample_url.
sampleAttributeId.
sampleAttributes.
sampleCode.
sampleDAO.
sampleId.
sampleId.
sampleId.
sampleLinkId.
sampleLinks.
sampleReportDAO.
sampleReportService.
sampleReportService.
sampleReportService.
sampleReportService.
samples.
samples.
samples.
samples.
sampleSearch.
sampleSearchAttributeId.
sampleSearchAttributes.
sampleSearchId.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleService.
sampleType.
sampleUrl.
score.
selection.
sender.
sequencer_run_url.
sequencerRun.
sequencerRun.
sequencerRun.
sequencerRun.
sequencerRunAttributeId.
sequencerRunAttributes.
sequencerRunDAO.
sequencerRunId.
sequencerRunId.
sequencerRuns.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunService.
sequencerRunValidator.
sequencerRunWizardValidator.
sequenceSpace.
seqwareRevision.
seqwareVersion.
server.
sessionFactory.
sharedStudies.
sharedWorkflowRuns.
shareExperimentId.
shareFileId.
shareLaneId.
shareProcessingId.
shareSampleId.
shareStudyId.
shareStudyService.
shareStudyService.
shareWorkflowRunId.
shareWorkflowRunService.
shareWorkflowRunService.
site.
size.
size.
skip.
skip.
skip.
skip.
skip.
skipTxt.
slideOneFilePath.
slideOneFilePath.
slideOneLaneCount.
slideOneLaneCount.
slideTwoFilePath.
slideTwoFilePath.
slideTwoLaneCount.
slideTwoLaneCount.
sortKeySample.
source.
source.
spotDesignReadSpec.
sql.
start.
startDate.
startPage.
startPosition.
startPosition.
startPosition.
state.
stats.
status.
status.
status.
status.
status.
status.
status.
status.
statusCmd.
statusCounts.
statuses.
stderr.
stdErr.
stderr.
stdout.
stdOut.
stdout.
stdoutFile.
stop.
stopPosition.
stopPosition.
stopPosition.
store.
store.
store.
storeType.
strand.
strand.
strategy.
strExpectedNumberReads.
strExpectedNumberRuns.
strExpectedNumReads.
strExpectedNumRuns.
strLaneCount.
strRefLane.
strStartURL.
strStartURL.
studies.
study.
study.
study.
study.
study.
study.
study.
studyAttributeId.
studyAttributes.
studyDAO.
studyId.
studyId.
studyLinkId.
studyLinks.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyService.
studyTypeDAO.
studyTypeId.
studyTypeService.
studyTypeService.
sum.
summaryLines.
svType.
swa.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
swAccession.
tag.
tag.
tag.
tag.
tags.
tags.
tagSetIDs.
tagSpec.
taskGroup.
template.
template.
templateFile.
templatePath.
templateType.
testCmd.
thickEnd.
thickStart.
timeTaken.
SETTINGSFILENOTFOUND=13
tissSource.
title.
title.
title.
total.
totalPrice.
totalUnits.
transcriptId.
translatedSequence.
translocationDestinationContig.
translocationDestinationStartPosition.
translocationDestinationStopPosition.
translocationType.
type.
type.
type.
type.
type.
type.
type.
type.
typeNode.
unit.
units.
units.
units.
units.
units.
units.
units.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimestamp.
updateTimeStamp.
updateTimeStamp.
updateTstmp.
updateTstmp.
updateTstmp.
updateTstmp.
updateTstmp.
updateValidator.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
url.
urlLabel.
urlLabel.
urlLabel.
urlString.
useIparIntensities.
useIparIntensities.
useOneURL.
username.
userName.
username.
useTwoURL.
useURL.
uuid.
validationReportService.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
validator.
value.
value.
value.
value.
value.
value.
value.
value.
value.
values.
version.
version.
version.
version.
visibleParams.
wfRuns.
workerName.
workerName.
workflow.
workflow.
workflow.
workflow.
workflowAccession.
workflowAttributes.
workflowDir.
workflowId.
workflowParam.
workflowParamId.
workflowParamId.
workflowParams.
workflowParamService.
workflowParamService.
workflowParamService.
workflowParamService.
workflowParamValueId.
workflowParamValueService.
workflowParamValueService.
workflowParamValueService.
workflowRun.
workflowRun.
workflowRun.
workflowRun.
workflowRun.
workflowRunAttributes.
workflowRunByAncestorWorkflowRunId.
workflowRunId.
workflowRunId.
workflowRunId.
workflowRunParamDAO.
workflowRunParams.
workflowRunProcessings.
workflowRuns.
workflowRuns.
workflowRuns.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflowRunService.
workflows.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
workflowService.
zygosity.
SIZE_COUNT_FILE=5
SIZE_COUNT_TREE=20
SNV=1
SORT_NAME="sortname"
SORT_NAME="sortname"
SORT_NAME="sortname"
SORT_ORDER="sortorder"
SORT_ORDER="sortorder"
SORT_ORDER="sortorder"
SORT_ORDER_ASC="asc"
SORT_ORDER_ASC="asc"
SORT_ORDER_DESC="desc"
SORT_ORDER_DESC="desc"
SQLQUERYFAILED=82
START_ALL_QUERYDATELONG="start-ALL_query-date-long"
START_PMC_QUERYDATELONG="start-PMC_query-date-long"
START_PMCSI_QUERYDATELONG="start-PMCSI_query-date-long"
START_QUAL_QUERYDATELONG="start-QUAL_query-date-long"
STARTCOUNTDATELONG="start-count-date-long"
STARTDUMP_QUERYDATELONG="start-dump_query-date-long"
STDOUTERR=90
STRING=24
STRING=24
STRINGID=20
STUDY_ATTRIBUTES="Header.STUDY_ATTRIBUTES.getTitle()"
STUDY_ID="study_id"
STUDY_ID="study_id"
STUDY_PREFIX="study_"
STUDY_SWA="Header.STUDY_SWA.getTitle()"
STUDY_TAG_PREFIX="Header.STUDY_TAG_PREFIX.getTitle()"
STUDY_TITLE="Header.STUDY_TITLE.getTitle()"
STUDY_VIEW="redirect:/myStudyList.htm"
SUBMITTED="submitted"
SUCCESS="success"
SUCCESS=0
SUCCESS="success"
SUCCESS="success"
SV=4
SV_COMPLEX=1
SV_DELETION=2
SV_DELETION_AND_INVERSION=3
SV_DISPERSED_DUPLICATION=4
SV_DUPLICATION_AND_INVERSION=5
SV_INVERSION=6
SV_LOCATION_DOWNSTREAM=2
SV_LOCATION_UNKNOWN=0
SV_LOCATION_UPSTREAM=1
SV_TANDEM_DUPLICATION=7
SV_UNKNOWN=0
T__26=26
T__26=26
TABLE_MODEL="tablemodel"
TABLE_MODEL="tablemodel"
TABLE_SEL="tablesel"
TABLE_SEL="tablesel"
TAG=10
TAG_CHAR='n'
TAGSETS_PARAM='s'
TEST_TABLE_PREFIX="Constants.Term.NAMESPACE.getTermValue(S"{trunked}
tokenNames="new String[] {, , ,"{trunked}
Category.debug(Object).
Category.debug(Object,Throwable).
TRANSLOCATION=5
TRANSLOCATION_COMPLEX=3
TRANSLOCATION_INTERCHR=2
TRANSLOCATION_INTRACHR=1
TRANSLOCATION_UNKNOWN=0
TYPE_TREE="sr"
TYPE_TREE="st"
TYPE_TREE_COMPLETED="wfr"
TYPE_TREE_RUNNNING="wfrr"
Unclassified=1
UNKNOWN="unknown"
UNKNOWN=130
UNKNOWN_TYPE=0
UNKNOWN_ZYGOSITY=0
VALUE_SEPARATOR_PARAM=','
VARIENT=0
VCF="VCFVariantImportWorker.VCF"
VCF="VCF"
VCF_CALLED_BASE="call_base"
VCF_CONSENSUS_BASE="con_base"
VCF_FILTER="filter"
VCF_HETEROZYGOUS="heterozygous"
VCF_HOMOZYGOUS="homozygous"
VCF_INFO="info"
VCF_READ_COUNTS="read_count"
VCF_REFERENCE_BASE="ref_base"
VCF_SECOND_ID="id"
VCF_SNV="SNV"
VERSION="0.7.0"
Category.warn(Object).
Category.warn(Object,Throwable).
WHITESPACE=25
WHITESPACE=25
WORKER_CHAR_PARAM='w'
WORKFLOW_NAME="Header.WORKFLOW_NAME.getTitle()"
WORKFLOW_RUN_NAME="Header.WORKFLOW_RUN_NAME.getTitle()"
WORKFLOW_RUN_PREFIX="wfr_"
WORKFLOW_RUN_STATUS="Header.WORKFLOW_RUN_STATUS.getTitle()"
WORKFLOW_RUN_SWA="Header.WORKFLOW_RUN_SWA.getTitle()"
WORKFLOW_SWA="Header.WORKFLOW_SWA.getTitle()"
WORKFLOW_VERSION="Header.WORKFLOW_VERSION.getTitle()"
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